1. Zelena - loved her, both in her main arc (3B) and as a "casual villain" in later seasons (the "Hi guys" in 5x07 was especially awesome)
2. Cruella - she was never a real threat or something like that, but she was funny, plus bonus for being the exception to the "Evil isn't born, it's made" rule.
3. Cora - also great. Her arc in season 2 was very good and her returns were also perfect. She was very cruel but also somewhat sympathetic.
4. Rapunzel - I'm probably in minority here, but I loved her arc in the beginning of s7. She felt threatening, even though she wasn't. Plus, her not being exactly magical (except for the wand) was also something refreshing. I mean, yes, her character kind of changed from 7x01 (where she killed the Fairy Godmother AND the Prince without blinking an eye) to 7x09 where she had the most sympathetic backstory and wasn't much of a villain.
5. Evil Queen - in season 1 she was perfect. Her team up with Cora in season 2 was... understandable, but I think 2x20 kind of destroyed her character, because it put her in a level of evil so high, committing genocide in the past and planning to commit it again in the present, so her redemption (two eps later) felt forced. Her return in s6 was amazing, until she just gave up her plan of dividing the heroes in 6x06.
6. Peter Pan - he was also very good. Threatening and refreshing, because Peter Pan being a villain isn't exactly something you see everywhere. His arc wasn't exactly the best one, but he was a great villain and his return in s5 was also good.
7. Gothel - Gothel was one of the few not-redemeed villains who last the entire season, so bonus for that. She was threatening and fun, but the problem with her is that her arc was basically abandoned in 7B because of the useless Candy Killer storyline. Plus, the writers probably didn't specify her plan, as both Drizella and Facilier mentioned she wanted the dagger and then... she actually didn't.
8. Drizella - I loved her as a villain in the beginning but when she just became "I want Ana's magic", it was kinda forced. Still a great character, though.
9. Rumplestiltskin (Wish Realm) - he wasn't exactly a main villain but was the final villain of the show, so he deserves to be here. I think he was good, but should have had more development. He literally came out of nowhere with a random plot and his goal was... getting rid of the heroes, who didn't really care about him? He should've just wanted the dagger.
10. Ingrid - she was a great character, but her shattered sight plan was a forced way to include something from the original fairytale. It was like, "I want to be with my sisters, why not kill the whole town? Yay".
11. Arthur - he was... good? I mean, Arthur was not much of a villain, at least for the OUAT standards. But his redemption was good, so...
12. Hook - he was a great secondary villain in s2 (kind of like Cruella), but the Dark Hook arc was just... No.
13. Maleficent - sooo much wasted potential here. Honestly, the "lost daughter" storyline was a bit disappointing since it could have been done with literally any other villain, and had nothing to do with Sleeping Beauty. And we never got to see her backstory.
14. Hades - was a good villain, but suffered from lack of backstory too.
15. Rumplestiltskin - he was great in the first seasons, but then his season 4 villain arc destroyed his character, and his 5B/6A arc even more. They should've just killed him in 3x11. At least season 7 gave him justice XD
16. Black Fairy - sooo much wasted potential here². As the creator of the Dark Curse and the villain who was "teased since s1", you'd imagine she would have a good backstory and clear motivation. But it was just like "I know the Savior is gonna kill me, so... let's face her! Nothing can go wrong". And we never got to see how she turned evil in the first place.